Shadow Alchemist
by Yizuki
Summary: Alchemy:The power to alter the natural world. Two brothers dabble in it to grant a wish. One loses an arm and leg. THe other is a soul in armor. Now they seek for the one thing that can change them back. The philosophers stone. Fullmetal Alchemistcrossove
1. Introduction

Okay. I decided to rewrite the story Shadow Alchemist. It's still the same, only with different characters playing different parts. But first! A disclaimer!

Disclaimer: I do not own Yugioh, Fullmetal Alchemist, or even Aqua. He is the property of Rose Mistress and Yugi, who is his lover.

Chapter 1: Characters

Edward Elric: Yami Jewelstone(Sorry I can't be more creative. Rose Mistress, if you're reading this I do know that that's Ruby's last name. I'm sorry. I couldn't think of anything else.

Alphonse Elric: Aqua Jewelstone(Again, Rose Mistress, if you're reading this, I'm not trying to steal your characters. I just thought that Yami and Aqua would go with this story really, _really_ well. Gomen nasai.)

Van Hoenheim: Atemu

Hoenheim: Atem

Winry Rockbell: Yugi Mouto

Pinako Rockbell: Sugoruko Mouto

Colonel Roy Mustang: Seto Kaiba(Seriously, he's the only guy with enough ambition(though it is hard to imagine him acting like a fool and chasing after women))

Lt. Riza Hawkeye: Isis(Ishizu)

2d Lt. Falman: Tristan Taylor

Breda: Malik (The hikari)

Jean Havoc: Joey Wheeler

Maes Hughes: Himself (For now. If you guys can think of a Yugioh character that can play his part, let me know.)

Lust: Mai Valentine(She's perfect for the part! )

Envy: Marik(The yami)?

Gluttony: Himself (Again. This is only temporary.)

Pride: Mokuba(I know he's just a kid, but if remember in season zero, he wasn't the nicest guy. I figure he'll do. Even if he is Seto Kaiba's brother…..hmmm….not there's something I could play with.)

Wrath: Dartz?

Sloth: Ushio (A much better choice to Rapheal in my opinion! )

Greed: Pegasus

Scar: Bakura(The yami)

That's all I can come up with. I hope you'll enjoy this new story!


	2. The Two Alchemists

Chapter 1: The Two Alchemists

House stood on the top of a house, glowing with an unearthly light. A lone voice screamed out into the night.

"Aqua!! Aqua?!" The room was dark and filled with many manuscripts and shelves of books. "Damn. Damn! How could this have happened!?" A young boy with pale skin and tri colored hair kneeled in front of a large symbol on the ground. His teeth were clenched tight, blood red eyes burning into the opposite wall. "It…it wasn't supposed to happen this way!" He clenched his fist and pounded on the ground. "No…HE'S GONE!!" The boy sobbed at the pain, his left leg gone all the way up to his knee, dark blood staining the ground and tainting the rune.

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It was a brutally hot and sunny day with several dunes of the desert scattered as far as the eye can see. A pale skinned teen aged boy with tri colored hair staggered forward. His hair was coal black, edged in maroon with golden bangs, two of which shot up into his hair like lightning. Dull red eyes looked at the landscape in fatigue. "I'm so hungry." He groaned and flopped back onto the sand. "At least if there was some grass I could turn it into bread and eat it." After laying there for a moment he looked around. "Aqua? Aqua! Where are you? Aqua? Aqua?!"

"Down here!" A white gloved hand shot out of the sand. The teen jumped as it grabbed a hold of his ankle. "Help me brother!" The teenager slowly turned his head to the gloved his in the sand.

"You sunk again?"

A moment later there was a huge pile of sand off to the side, with heavy breathing as the predominant sound. The teenager was bent at the knees, standing next to an elegant suit of black armor chased with gold, small rubies and aquamarines used for decorations and strength on the critical parts. A black helmet was shaped a bit like a dragon's head, two slits made for the eyes. From there two red sparks gleamed out at the world. A dark red cape draped across his back. The teenager looked at the suit of armor, which was at least three heads taller than him, and gave it the stink eye.

"If you do that again I'll leave you behind!" He shouted.

"But…" The suit of armor stared.

"No buts!" He punched the chest plate. It fell off and dumped sand onto him. "Aqua….." The suit of armor started scooting away. The teenager burst out of the sand and began chasing him in circles. "Wait Aqua!"

"No I won't wait!" He cried.

"Stop!"

"No I won't stop!"

"Do one of them!" The teenager cried.

"I can't decide on one!" Aqua shouted back.

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Now the two brothers were in a city decorated with numerous statues of a man holding a staff that had the sun on top with the head of a hawk. The place was obviously prosperous, as could be seen by the clean streets and well kept for buildings. The teenager and Aqua walked through the streets, the teen trying to maintain as much dignity as he could with as exhausted as he was. The white suit of armor looked at him in concern.

"Are you okay brother?" He glared at Aqua.

"It's your fault for not stopping." He grumbled. The armor, known as Aqua, gave a slightly nervous chuckle.

"I doubt that anyone would stop in that kind of situation, even if they're told to." The teenager snorted.

"Really? That's nice." He sighed. "I'm thirsty…." He stopped as he caught the soft sound of liquid pouring somewhere. He blinked and ran to the nearest street. At the end was a fountain pouring some sort of liquid into the basin. "Water." He brightened and began running toward it. "It's water!" Aqua reached out toward him.

"Big brother!" The teenager was about to launch himself into the liquid when he stopped. He gripped the edge of the fountain and looked down at the red liquid forlornly.

"So this is what I smelled earlier." Aqua ran up to where his brother was. He looked at the liquid with confusion.

"Blood?" He asked. The teenager dipped a cup into it. He closed his eyes and gave a small smile.

"It's red wine."

"Hey!" They both looked over to one of the side streets. A man with a large mustache was glaring at them. "Children aren't allowed to use this place!" A moment later he was laughing. "I'm sorry! Travelers like you wouldn't have known there's a spring of wine." The teenager shrugged.

"Lior city must be wealthy to have a fountain of wine." He drank gratefully from a glass filled orange soda. The man studied the two closely.

"….You're not street performers are you?" The teen sprayed soda everywhere. He spluttered and glared at the mustached man.

"Old fool! What makes you think that?!" He shouted. The man looked slightly flustered.

"Well….I mean….what else could you be?" He asked. "I haven't seen your faces around here before. On a trip?" The teenager smiled slightly.

"You could say that. We're looking for something. The man nodded the seemed to perk up and look at his watch. He turned to the radio and turned it on, tuning it in to a specific frequency. Serene, calming music played. Aqua and the teenager looked at the radio in interest. A deep voice began to speak.

"_Children of god who dwell on earth. There is no salvation without prayer and faith. The sun god Ra will illuminate thy path. Behold! The lord hath descended from his heavenly throne to save the from all thy sins."_ Aqua lowered his head as he listened. _"For I am thy father…I am the emissary of the sun god." _Aqua turned to the man.

"A religious broadcast on the radio?" The teenager looked doubtfully at the radio.

"Emissary of the sun god?" He asked disbelievingly. "What the heck is _that_?"

"You've never heard of father Cornello?" The two looked at him blankly.

"…Who?" It was the man's turn to stare at them.

"Father Cornello, the sun god's emissary!" Other men gathered around them, more than one with a beer glass in hand.

He's the founder of the church of Ra. He can work miracles!"

"He's a wonderful man who came to this town a few years ago and showed us the way of god!" Another piped up.

"Yeah! He's amazing!" Another shouted.

"They're real miracles! It's the work of God!" The tri colored haired teenager just yawned. The moustached man got a vein on his head.

"Are you even listening boy?!" The teenager shrugged.

"Nope. I'm agnostic.(1)" He got up easily. "Well, thanks for the food. Let's go." Aqua nodded and began to get up as well.

"Okay." His head bumped into the ceiling and the radio lost balance and fell to the ground where it broke.

"AAAAAH!" The man shouted.

"Oops." Aqua said. The man rounded on him.

"Hey! Could you _please_ be more careful sir? Frankly, you shouldn't walk around wearing that suit…." The teenager held up his hands.

"It's our fault. We'll fix it right away." The man calmed and raised an eyebrow.

"You think you can fix it?" The teenager nodded.

"Just sit back and watch." Aqua knelt to the ground and began drawing a symbol on the ground around the radio. When he had finished there was a perfect circle drawn into the dirt with a pentagram in the center. "Okay! I'm all set!" He took a deep breath. Everyone watched with interest. Aqua crossed his hands. "Here we go…" Nothing happened for a moment, then a spark of lightning crashed down from his hands.

"Aagh?!" The people flailed back. A cloud of smoke lifted off the ground and surrounded the device. When it cleared the radio was repaired and broadcasting even more beautifully than ever. The teenager pointed to the radio.

"How's that?" He asked. Everyone just stared wide eyed at it.

"That…..That's amazing!" He turned to the two. "You can perform miracles?!" The teen looked at him funnily.

"Miracles?"

"We're just alchemists." Aqua said.

"We're the Jewelstone brothers. A lot of people have heard of us." Yami stated.

"Jewelstone eh…? The Jewelstone brothers?" One asked.

"I've heard of you guys!" A man declared.

"They say the older brother is a state alchemist they call…..The Shadow alchemist Yami Jewelstone!" All the people rushed towards them. Yami closed his eyes in pride.

"So you're the master alchemist that everyone's talking about!!" One said to Aqua.

"Oh, I see. It's because of the color of your armor eh?" Aqua laughed embaressadly.

"Uh no….It's not me…It's him." They all looked toward Yami.

"You mean the little guy?" Yami stiffened, his head bowed so that you couldn't see his eyes. Then he looked up and exploded.

"I'M NOT LITTLE! DON'T CALL ME MIDJET! OR SHORTY! OR SHRIMP!" He began flinging them around. The terrified villagers ran away.

"We didn't say any of that!" They shouted desperately. Aqua stood calmly behind his brother.

"I'm the younger brother, Aqua Jewelstone." Yami stepped forward aggressively.

"It's ME! I'm the 'Shadow Alchemist'!! Yami Jewelstone!!" They all stared at him in fear.

"S….Sorry about that…." A young girl ran toward the small shop where everyone was. She stopped and smiled at the store owner.

"Good day sir. My, you're busy today." The man looked toward her.

"Oh hello, Rose. Going to the temple today?" The girl nodded, pink bangs contrasting starkly with her brown hair. Warm, sparkling brown eyes smiling at everyone.

"Uh-huh, with some offerings." She held out the necssary money. She noticed Yami and Aqua. "Oh, new faces…" The store owner nodded.

"Yeah. They say they're alchemists and that they're looking for something." She took what the store owner had given her and smiled at them.

"I hope you find what you're looking for. May Ra bless you!" With that she walked off. The store owner watched her go off with a fond look.

"Rose-san's become so happy lately." He said. One of the customers nodded.

"Yes, and it's all thanks to the father." Yami looked at them.

"Huh?"

"Not only does she not have no family, but she lost her boyfriend last year in an accident…" The store owner explained.

"It was hard to see her so sad. I felt really bad for her." Another customer said.

"That's when she was saved by father Cornello! He taught her about the sun god Ra!"

"Preach on! He raises the dead, and the souls of his faithful live forever. Cornello's miracles prove it."

"You should see them for yourself! It's definitely the power of god!" Yami looked into the distance, his eyes lost somewhere even farther away.

"'Raise the dead' huh? I don't like the sound of that….."

"_I tell you, pray and have faith. All thy prayers will be answered."_The radio said.

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"And the grace of his light shall shine upon all of his children." An aged, bald man read from a book in a luxurious study. With this final line, he closed the book and turned off the speaker. A man with a hand towel and a glass of water stepped forward. He was large with pronounced muscles and a black beard pair with short clipped hair.

"A fine sermon your holiness." He said.

"Yes, thank you, your holiness! It's always an honor to hear you preach." Another commented.

"Your holiness!" At the door to the study was Rose, waiting anxiously to speak to the priest. Cornello smiled and got up from his chair.

"Oh, It's you Rose. My, so dedicated! You're an example to us all." She blushed.

"No, I'm just doing my duty." She said. She looked down at her hands. "Um…by the way, father…." Cornello smirked.

"Yes, I know what it is you ask. God has seen your good deeds." She brightened considerably.

"Then…." She said breathlessly. He put a hand on her shoulder.

"But it isn't _time_ yet Rose. You understand don't you?" She looked down.

"…..Yes, father….You're right….Not yet…." Cornello smiled.

"That's a good girl Rose."

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In the main room of the chapel, Yami and Aqua stood and looked at a statue dedicated to the sun god Ra at the end of the long row of pews. Rose came through a side door and her face lit with recognition as she saw the two.

"Oh, It's you two again! Are you going to join the church of Ra?" She asked. Yami smirked sadly.

"Naw….Sorry, but I'm not religious." Rose shook her head.

"That's not a real answer! If you believe in god, you can live with hope and gratitude every day. It's wonderful!" She closed her eyes in rapture as she spoke. Then she opened her eyes and they had a mischevious glint in them. "If you have faith you'll grow taller for sure!" She declared. A vein appeared on Yami's head.

"What was that?" Aqua held him back.

"She's not saying it to be mean." He said placatetingly. Yami sighed and sat down.

"Sheesh…How can you honestly believe these things?" He asked. "Do you really believe that if you pray to God the dead will come to life?" She stood straight and proud as she declared her answer.

"Yes. I do!" Yami lowered his head and sighed heavily. He pulled out a tiny book filled with small scraps of paper as markers and opened.

"Water: 35 liters. Carbon:20 kilograms. Ammonia: 4 liters. Lime:1.5 kilograms. Phosphorous: 800 grams. Salt:250 grams. Saltpeter: 100 kilograms. Sulfur: 80 grams. Fluorine: 7.5 grams. Iron:5 grams. Silicon:3 grams, and over fifteen other elements in small quantities." Rose just looked at him with a confused expression. "That's the total chemical makeup of the average adult body. Modern science knows all of this, but there has never been a single example of successful human transmutation." He looked to Rose. "It's like there's some _missing ingredient_…scientists have been trying to find it for hundreds of years, pouring tons of money into research, and to this day they don't have a theory." He closed the book with a snap. "They say science is a lost, but I think it's better than sitting around praying and waiting for something to happen." He gained an amused expression now. "For that matter, the elements found in a 

human being….is all junk you can buy with the allowance of a child. Humans are so cheaply made." Rose looked livid now.

"People aren't _objects_! That's an insult to the creator! God will punish you for saying things like that!!" Yami laughed.

"Alchemists are scientists. We don't believe in uprovable concepts like 'God'. We strive to uncover the principles of creation in the matter of the world, to pursue the thruth…." Now he got up and looked up at the statue. A sad smile graced his lips. "It's ironic that we scientists…who don't believe in god…are in a sense the closest things to him." Rose glared at them coldly.

"What pride….Are you saying that you are gods equal?" Yami sat back down.

"Ra is the god of the sun…but what is the sun really? Just a chunk of light and immense heat." He closed his eyes. "You get burned if you get too close to the sun." Again, Rose was confused.

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Cornello stood on a platform above a crowd of people with flowers falling all about. He caught one in his hand and transformed it into a gigantic sunflower. The people roared at the display. Cornello just kept waving.

"….What do you think?" At the very back were Yami and Aqua. Yami, much to his embaressment, having to stand on a wooden box to see above the crowd.

"That kind of transmutation has to be alchemy." Aqua commented. Yami nodded.

"That's what I thought too." Aqua looked to his brother.

"But what about the laws?" He asked.

"So you came after all!" They both turned to see Rose only a few feet away. "See?! He _does_ have miraculous powers. Father Cornello is the sun god's child!" Yami stroked his chin.

"No….that's definitely alchemy. No matter how you look at it. Cornello's a fraud." Rose growled.

"But he can bypass the laws for some reason." Aqua commented to keep the peace. Yami nodded.

"Yeah…that's the problem right there."

"The Laws?" Rose asked. Yami pointed upwards.

"Most people think that alchemy can do anything and create whatever you want….But in reality there are certain concrete laws. I guess the two big concepts are "The law of conservation of mass" and "The law of natural providence." Although some alchemists conjure with the four elements, or with the three principles…." Rose looked completely confused. Aqua sweat dropped.

"Umm…let me try. A substance can only be created from the same type of substance. For example, if something's mostly water, you can only use it to make other things with the same attributes of water."

"In other words…" Yami started again. "The basics of alchemy is the 'equivalent exchange'! That means that to obtain something, something of equal value must be lost." He glared at Cornello. "But that Old 

man is making too much out of too little…alchemy wise, that's breaking the law." Rose looked vindicated.

"So they are miracles!" Aqua looked up at the stage uncertainly.

"Big brother….do you think…?" Yami nodded.

"Yes….I do. I think we've found it." He turned to Rose. "Hey! I'm starting to get interested in this religion! I'd _love_ to speak to his holiness. Do you think you could take me to him?" Rose squealed and clapped her hands.

"Oh my! So you're starting to believe!"

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Back at the church, the man who had given father Cornello his water after his sermon came into the room.

"Your holiness. There are some people here who are requesting an audience with you. It's a boy and a man in a suit of armor. They say they're the Jewelstone brothers…." Cornello looked up from his cup of tea.

"What? I'm busy. Send them away." Then he stiffened. "Wait…Jewelstone brothers..Yami Jewelstone!" The man nodded.

"Yes. It was the boy who called himself that…do you know him?" Father Cornello was not listening.

"Aagh! This is bad!" He looked up to the assistant. "It's Yami Jewelstone…the 'Shadow Alchemist'!" The assistant started.

"Wha….But he's a little brat, only up to my chest! You're joking right?!" Cornello pinched the bridge of his nose.

"Fool! Alchemical skill has nothing to do with age!" He sighed. "I had heard that he obtained he title of state alchemist at the age of 12….So…The rumors about this brat were really true." The assistant looked angry.

"What is a state alchemist doing here?! Could it be that our plan…"

"It seems the dogs of the military have good noses." Cornello said.

"Shall we chase them away?" The man asked.

"No, that would cause them more suspicion. And even if we did chase them away, they'd come back…and bring more." He smirked. "Let's just say they were _never here._" The assistant looked confused for a moment before an evil grin cracked across his face.

"It shall be as god's wills." He said.

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The man who had talked with Father Cornello led Yami, Aqua, and Rose to an almost empty room.

"His holiness is very busy. So it's not easy to get an audience with him. You two are very lucky." Yami smirked.

"I'll try not to talk for too long." He said. The man smirked and reached into his coat.

"Yes, Let's end it right away." He put the gun to Aqua's head. "Like this!" He pulled the trigger and Aqua's head went flying off. Yami watched in shock for a moment as the helmet clanged on the floor. The two guards in the room pointed their weapons at his throat. Yami was trapped between the spears and the two guards. Rose turned to the assistant.

"Brother Cray! What are you doing?!"

"Rose, these are heathens that were trying to entrap his holiness. They're evil." She gasped.

"What?! But his holiness would never let you do this…let you..." He smirked at Rose.

"He did allow it! The words of his holiness are the words of god." He aimed his gun at Yami's head. "This is the will of god!" He shouted. Yami chuckled.

"Guess there's some really bad god's out there." Aqua, with his helmet still off, got up and gripped Cray's gun. The man paled as he looked inside.

The entire suit of armor was hollow, with nothing in it, not even strings to suggest a puppet master.

"Wha?!" Cray shouted. Yami grabbed one of the guards under the arm and threw him to the floor. Aqua punched Cray in the face while Yami took on the guards.

"Aaaggh!" One shouted. Yami threw Aqua's helmet/head at the man, knocking him out cold. Yami punched the air in victory.

"Strike!" He shouted.

"My head!" Aqua cried out. Rose screamed.

"Wh-wh-wh….WHAT IS THIS?!" Yami tapped his brothers chest, letting the hollow sound echo for a moment.

"Nothing special….Just what it looks like." She held her hands to her face.

"Th-there's nothing inside…It's empty!?" Aqua sighed and put his head back on.

"You might say…that this is what happens when you commit the greatest sin….when you trespass in god's domain. My big brother and I both…" Yami was turned away from them, as if ashamed. Rose looked at him.

"You too….Yami?" Yami sighed and scratched the back of his head.

"Well, let's just save that story for another time…." He looked down at Cray with disgust. "Anyway, I guess your god showed his true colors." Rose shook her head.

"No! It has to be some kind of mistake." Yami snorted.

"You've seen all this and still believe in 'his holiness'?" He turned to her. "Rose….Do you have the courage to face the truth?"

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Yami and Aqua stood outside a pair of double doors. Yami gazed at them with distaste.

"Is this Cornello's room? The one that Rose told us about?" Aqua asked. Yami stepped forward.

"Let's find out." The doors opened for them. It was completely dark inside. Yami snorted.

"Hmph. I guess that means 'come on in'." They both stepped into the room. As soon as they were a fair distance from the door, it slammed shut.

"Welcome to the church of the great Ra." A voice echoed. Yami and Aqua looked to the far end of the room. Cornello stood on a set of stairs at the far end of the room. "Did you come to hear me preach? Hmm?" Yami smirked.

"Yeah…By all means….Teach us…Like how you use your lame alchemy to deceive your followers!" Cornello just kept smiling.

"Well…I'm not sure what you mean. Please don't confuse my miracles with alchemy. If you saw for yourself you'd believe…"

"Yeah. I have seen it all right." Yami interjected. "What I can't understand was how you were able to do transmutation that goes against the laws." Cornello chuckled a bit.

"That's why I'm telling you it's not alchemy."

"And then it came to me…" Yami continued, as if he hadn't heard the man. "The philosophers stone. _That's_ how you do it, right?" Cornello scratched his head. Yami gazed at him. "Like maybe…just maybe…that ring? Cornello lowered his hand.

"Heh. The government get's their money's worth out of you don't they? I guess you saw through the whole thing." He smirked. "Correct! The philosophers stone, the legendary catalyst, the amplifier of all alchemical processes. With this, I can conjure at the minimum for the maximum result!" Yami got a mad glint in his eyes.

"How long I've searched for that…"

"Hmph! What's the jealous look in your eyes?! What do _you_ want the stone for? Money? Honor?"

"What about you? What do you get out of founding this phony religion?!" Yami shot back. "If it's money you want you can make as much as you want with the stone." Cornello laughed.

"It's not about the money. Well, I do want money, but I can get that with almost no effort….in the form of donations from my flock." He stroked his chin. "What I _really_ need are followers who will happily give their lives for me." Stood proud and tall as he continued. "Think about it! An invincible army of fanatics with no fear of death! Soon I'll have more than enough people! Just watch! Within a few years time this entire nation will be mine!" Yami exploded with laughter. Cornello spluttered at his obvious mirth.

"Well that's fine, but I don't really care about that." He stated.

"WHAT!!" He shouted. "DON'T BELITTLE MY AMBITIONBY SAYING 'YOU DON'T CARE'! You'd better care! You're a member of the military after all!" Yami stuck a finger in his ear and twisted it.

"You know, to be honest, I could care less about my country _or_ the military." He pointed his finger at Cornello. "I'll be blunt! Give me the philosophers stone! If you do that I'll stay quiet about the scam you've been pulling on everybody." Cornello laughed.

"Hah! You'd try to bargain with me? My followers would never listen to the words of an outsiders like you! The people of this town love me! They think that my words come from god! No matter how much noise you make, no matter what evidence you have, they'll _never_ listen to you!" He was lifting off ground in his ecasty. "THOSE IDIOTS WILL BELIEVE ANYTHING I TELL THEM! I'VE COMPLETELY FOOLED THEM!" Yami clapped his hands.

"Wow. You're _really_ smart. Telling me how you do it." He folded his arms calmly. "You're right. Your followers would never listen to a word I say. But!" Aqua began to take off his chest plate. Yami jerked his thumb at them. "What about her words?"

Rose was sitting there in Aqua's armor with wide, scared eyes, looking at father Cornello with disbelief.

"R-Rose?!" Cornello spluttered. "What is the meaning of this?!" Rose scrambled out of Aqua.

"Father! Is everything you said just now true?! Were you fooling us this whole time?! Your miracles aren't real?! The power of god can't grant my wish?!" Tears were threatening to fall from her eyes. "YOU CAN'T BRING MY DARLING BACK AGAIN?!" Cornello just stared at them in disbelief for a moment, before smiling.

"Hmm…It's true that I'm not god's emissary…but with this stone, it may be possible to transmute living beings, which so many alchemists have tried and failed." He stared directly at her, as if he was trying to hypnotize her. "Rose. I will resurrect him!"

"Rose, please don't listen to him!" Aqua shouted. Cornello held out his hand.

"Rose. Be a good girl and come here." She looked between the two. Yami stared at her with hate.

"If you go, you can never come back!" He stated. Cornello kept smiling and beckoned her.

"What's the matter? You belong with us." He said in a fake sweet and tender voice.

"Rose!" Aqua shouted.

"I'm the only one that can grant you your wish. Isn't that so? Think about it darling. And come!" A bit of his lip peeled back to show his pearly white teeth. Rose bowed her head and began walking towards Father Cornello.

"I'm sorry you two." She said. "But this is the only choice I can make." Cornello stared down at them haughtily.

"You truly are a good child." He commented. Yami snarled at him. Cornello raised a hand. "Well then….now we must eradicate these heathens who threaten the future of our faith." He waved his hand at a door, which opened immediately. Yami looked at it warily. Growling and snarling noises came from inside. A reptilian tail lashed out from the darkness before it snaked back in. A moment later a monster with the head of a lion and the body of a reptile stepped out. "The philosophers stone is truly incredible…It can even create new life like this." He looked down at his creation. "Have you ever seen a chimera?" Yami ran appraising eyes over it.

"Looks like this one might be tough to deal with empty handed." He clapped his hands together. Cornello watched with interest. Yami slammed his hands onto the ground. The lightning that came from transmutation flared out. Yami stood up and held out his hand. Then, o the shock of everyone else, a spear began to rise from the ground. When it was fully out of the ground, Yami grabbed it and spun it so that the tip was pointed at the chimera. Cornello was shocked to say the least.

"You made a weapon from the floor without a transmutation circle?! You deserve the title state alchemist after all." The chimera began to charge. "But that still won't be enough!" The chimera sliced his spear in half and grazed his leg. Yami got on one knee with wide eyes. Cornello laughed.

"Ha! Ha! Ha! How do like the taste of claws that can cut through iron?!" Rose just watched in horror. Yami grinned madly.

"Psych!" He cut off all but one of his claws. Cornello stared in disbelief. Yami kicked the cat in the chest. Yami smirked at Cornello. "Sorry. These are custom made."

"Wh-what's the matter?! If your claws won't work then bite him to death!" The chimera charged him again with a roar. He sank his teeth into one arm, trying to crush the bones, but for some reason, they couldn't get through. Yami stood there calmly while the chimera still tried to bite his arms. He glared at the thing with a burning crimson gaze.

"What's the matter kitty? Taste bad?" He kicked the giant cat in the jaw, throwing it off of him. "Look at me Rose." Scraps of his trench coat fell down. "This is what happens when you use alchemy on humans…" Dark metal began to show on his arm. "This is what happens to sinners who trespass in god's domain!" Cornello stared.

"Auto-mail…full steel prosthetics….made from pure shadow ore." His eyes narrowed. "'Shadow' metal prosthetics….so that's why…The Shadow Alchemist!"

It was true. Half of Yami's leg and his entire arm was a prosthetic made out of pitch black metal that gleamed in the light. Faint tints of red and purple showed in indecipherable designs. Scars protruded out from where the metal met his body, like ties that kept it stable. He raised his metal arm.

"Come down here and face me you third rate fraud. I'll show you there's no comparison between us!" Cornello gazed at him.

"I see….Now I understand who you are…It was always a mystery to me why a mere brat had such a fearsome name as 'Shadow'….But now I know." He sneered at them. "Look at them Rose! Those two dared to do the one forbidden thing to alchemists…the unspeakable crime of human transmutation!!" Cornello snarled. "They've committed the worst possible sin!" Rose's eyes widened as she remembered what Yami had said.

"_You get burned if you get too close to the sun."_

Agnostic is someone who believes in a supreme being not within any established religion.

End Chapter


	3. The Price of Life

Chapter 2: The Price of Life

_(Flashback)_

"_Aqua! Aqua! Hey Aqua!" A miniature version of Yami races down the hall to find his little brother, scrolls and books falling from his arms in his haste. He bursts into a study filled with books and antique items. A young boy looks up from the only table in the room towards him. Well, actually, it was a young dragon, no bigger than a ten year old with scarlet eyes and a aquamarine set into his forehead. He looked to his brother who was scampering towards him._

"_What is it big brother?" Yami sets down a large diagram that he can barely stretch out onto the desk._

"_LOOK! We can't go wrong using this theory!" Aqua's eyes widened as he took in the information._

"_No way! This is…"_

"_IT IS!" Yami shouted in excitement. "This says how to do it! We can bring mom back from the dead!!"_

"We never had any doubts about doing it. Our mother was kind, the kindest person in the world."_ Yami and Aqua are looking into books and pointing out what they can add to their theory. _"All we wanted was to see our mother smile again…..Even if it meant breaking the laws of alchemy. It was the only reason we were studying alchemy after all……." Aqua bowed his head and sighed. "But the resurrection failed."

_Yami and Aqua are in the middle of an alchemical whirlwind, their body parts being slowly taken away by the magic._

"When it failed my brother lost his left leg….and I had my whole body taken. I lost consciousness for a while…."

_Yami is sitting against the wall with both his left leg and right arm missing._

"The next thing I saw when I opened my eyes was this armor body and a sea of blood."

_The suit of armor is kneeling next to the mutilated form of Yami, who is still using the wall for support. Yami chuckled darkly as he tried to bear the pain._

"_Heh, heh….Sorry. All I could get for one arm was your soul." He curled up in pain as the open wounds throbbed. His other arm gripped his shoulder where the missing appendage should be and ground his teeth to keep from crying out. Aqua just stared in disbelief._

"_Brother….why?"_

Now it's back to the present, with Aqua and Yami standing and looking at Rose and father Cornello.

"Even after the horrible injury of losing his left leg….My older brother exchanged his right arm for my soul….and put it in this suit of armor." His gloved hand went to touch his chest. "Sugorouko Gardner, our surrogate grandfather, had recently come up with a new auto mail. Shadow ore is considered too brittle and unstable to be used for anything except blast mining. But he had found a way to melt and temper the material so that it became metal harder than diamonds, tougher than iron, and more lasting than stainless steel." Yami closed his eyes and smirked.

"Heh. The two of us tried to resurrect one person and this is what happened…." Rose was still staring at them with a mixture of horror and disbelief. "This is what it takes to raise the dead Rose." He looked at her with his eyes full of fury, the fires from somewhere deeper than hell burning within them. "ARE YOU READY TO MAKE THAT SACRIFICE?!" Rose flinched away from him as his words sunk in. Cornello laughed and went to the edge of the railing.

"Heh, heh, heh! And you call yourself a state alchemist!! Don't make me laugh!"

"Bit late for that." Muttered Aqua. Yami however, was furious.

"Shut up!! You're just a third rate hack who can't do anything without that stone!!" Cornello chuckled.

"I see, I see…So _that's_ why you want the philosophers stone. Good Idea. If you used _this_, you might be able to transmute humans for _real_ eh?" Yami snorted.

"Don't get the wrong idea baldy! The reason we want the stone is to get our original bodies back!" He smirked as he rubbed his mechanical arm. "Besides, we still don't know if it'll even do _that_!" Aqua held out his hand.

"Father, I'll ask you again. Give us the stone before you get hurt." Cornello touched the cane and a small spark came from the stone. He chuckled.

"You fools are the ones who came too close to god and fell to earth…" He pulled his hand forward, transforming the cane into a giant machine gun. "If that's the case then this time I'll make sure to send you to god permanently!!" He began firing the huge gun at them, the sound of the bullets almost deafening. "Ha, Ha, Ha, Ha, Ha, Ha!" He laughed as the bullets continued to fly. Rose covered her head to try and protect her head from the shrapnel. Cornello stopped firing and waited for the smoke to clear so that he could get a good look at their dead bodies. His smug look however, was soon replaced with a shocked one. "Huh?!" A metal wall had been conjured up at the last minute and stopped the bullets from hitting either one of the brothers. From behind the barrier, Yami smirked.

"Sorry, god doesn't like me very much. Even if I went, he'd probably chase me away!" Cornello snarled. Aqua dashed out from behind the barrier and scooped Rose into his arms. Cornello turned to them.

"Why you…..!" He began firing the gun again. Aqua ran as fast as he could to avoid the bullets.

"Ow, Ow, Ow, Ow, Ow, Ow, Ow!" He cried as some ricotched off the armor. Rose just covered her ears and screamed. Yami was racing ahead towards the doors.

"Aqua! Let's get out of here!" Cornello laughed.

"Fools! The exit is rigged! Only I can open it from up here!" Yami smirked.

"Oh. Is that so?" He clapped his hands together. He put them on the wall and transformed a portion of it into another door.

"_Whaaat?!_" Yami crashed through the doors he just made and into a hall full of people.

"If there's no door I'll make one!" He raced down the corridor, Aqua, still holding Rose, right behind him. Cornello burst through the doors not long after.

"Don't just stand there! Go after them!" He shouted. "They're pagans who want to destroy our religion! Get them! Hurry!" The people immediately picked up weapons and chased after them.

"There they are!" One shouted.

"Hey you! Stop!" Another shouted. Yami and Aqua, who had been running towards them, skidded to a halt. The group smirked.

"Hey, you little runt, are you gonna take us all on empty handed?" One asked.

"Might as well give yourself up before you get hurt." Another said. Yami just smiled cheerily at them and clapped his hands together. The two who had talked to him before just stared blankly. Yami put one hand on his shadow mail, and with an evil smile, turned it into a wicked blade. Everyone became as white as a sheet. Yami beat them up with the blunt of the blade and his other fist, sending them flying 

down the hall. A group hiding in a side corridor watched them skid into view with trepidation. The leader sweated.

"Err….Umm….They're strong! Don't let your guard down just because he's a kid!" Aqua dashed into view and rammed into him, knocking him unconscious.

"'Scuse us." He said, not stopping for a moment. The man fell to the floor with a nose bleed and swirly eyes. Yami and Aqua continued to run until they passed an office who's door were wide open. Yami stopped and looked in.

"What's this?" He asked.

"The broadcasting room." Rose replied. "This is where father Cornello delivers his sermons over the radio." Yami got an evil look in his eyes as he stroked his chin.

"Oh really?" Aqua sweat dropped.

'_Uh oh. He's got a BAD idea.'_

_._

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………………………………………………………………………………………………………………………………………………………………….

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A man looked down at his watch.

"There sure is a lot of noise down there today isn't there…?" A man was holding a rope and looking up. Another man, who had just come up, shouted at him.

"Hey! What're you doing?! It's way past time for you to ring the bell!" The man just continued to look up. But he did respond a little.

"The bell…"

"Huh?"

"The bell's gone." The guy looked up with him.

"Say what?" Down on the ledge beneath the bell tower, Aqua sighed in relief, the bell on his shoulder. He walked over to part of the roof that was meant to be walked on. Rose was with him, standing a little off to the side so she wouldn't be in the way.

"About what you were saying before…I can't believe you have to do all that to perform alchemy." Aqua set down the bell, which made a faint 'gong'.

"I told you. The foundation of alchemy is the 'equivalent exchange'. To obtain something, something of equal value must be lost. People call my brother a genius, but the reason he's so good at it is because he paid the price…and worked so hard."

"But because you sacrificed so _much_, you must have been able to bring back your mother."Rose said with a hopeful face. Aqua looked down.

"…..The thing we brought back wasn't even human anymore." Rose's hope faded to horror and disbelief again.

_Flashback_

"_Nooo! How could this have happened? Big brother….your theory was flawless!" Yami chuckled bitterly in spite of his wounds._

"_Yeah…there weren't any mistakes in the theory…." He coughed, blood coming from his lips. Yami drew his hand away and looked at it. "We were the ones….who made the mistake."_

_End Flashback_

"We've given up transmuting humans, but my brother still wants to get me my original body." Aqua's now drawing a transmutation circle. "But like I said before, the risks are high…so we might end up even worse, or lose our lives. That's the way things are in this business." He stood up and looked to her. "Rose, that's why…you can't choose this path."

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………………………………………………………………………………………………………………………………………………………………….

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Cornello burst into his office, the doors banging against the walls he threw them aside with such strength. He glared at Yami, who was idly sitting on the desk, inspecting his fingernails.

"You little runt! You're not getting away!" Yami put his chin in his hand.

"Shut up will you? News of your trickery will soon spread throughout the town in no time anyway." Cornello snarled.

"Shut up! Everyone in the church is under my direct control! They'd never listen to a stupid follower even if she did contradicted me!" He heaved from his emotions and all the climbing and running he had had to do. Yami went back to examining his nails.

"My, my. I feel sorry for those followers of yours."

"Shut up! Followers are just pawns to be used for _war_! I don't have time to feel sorry for pawns!" He stood up straight. "Did you think you could stop my plans so easily?! You underestimated the power of blind faith!" Yami's lips quirked a bit.

"Heh. Heh, heh, heh, heh. Ah hah, hah! Aha ha, ha, ha, ha, ha, ha, ha!" Yami was close to falling off the desk in his mirth, rocking back and forth.

"What's so funny?!" Cornello asked. Yami chuckled.

"T-This is why I keep saying your third rate baldy!" Cornello snarled.

"You little brat! How dare you insult me!!" Yami held up a switch.

"Know what this is?" He asked in a singsong voice. Cornello stared at it for a moment, then paled.

"You…you couldn't have." He whispered. "YOU LITTLE RAT!!" Outside Aqua was holding the town bell out so that Cornello's voice rang throughout the entire city. Everyone was looking at the different places where radios and speakers had been placed, their faces caught between a look of utter shock, horror, or anger. "How long has that switch been on?!"

"From the very beginning!" Yami said in a sing song voice. "You just exposed your entire plan!"

"Wha..Wha…Whaaat?!" He shouted. Cornello bowed his head in rage. "You dumb brat…..I'M GOING TO KILL Y….!"

"Too slow!" Yami said, transforming his shadow mail arm into a simple extension blade and slicing through the gun Cornello had made his cane out of again. There was a loud clanking as the piece scattered across the floor. "Didn't I tell you? There's no comparison between us." A smirk played at his lips. Cornello growled.

"I won't….I won't give up!" He howled and began reconstructing the gun. "As long as I have the stone I can make miracles again and again!" Yami backed up a bit. All of a sudden he got the feeling that something was wrong. The sparks from his alchemy changed and shot up his arm and fused the metal into it. It looked as if shrapnel had embedded itself into his arm, but instead of bleeding, it grew out of the flesh. There was a moment when the man was silent, as if his brain hadn't caught up with what had happened. Then he howled in pain.

"GAGH! MY ARM! MY ARM! AAAGHHH! IT HURTS! IT HURTS! MAKE IT STOP! UGGGHH!" Yami growled and grabbed his robes.

"SHUT UP! It was just a rebound!! Don't make a big deal over one or two arms!!"

"Nhhhh…." He moaned.

"The stone! LET ME SEE THE PHILOSOPHERS STONE!!" Yami shouted.

"Aughh! M-my stone…." Cornello said. The said stone was cracking and broke free of the ring, landing on the ground and disintegrating into nothing. Yami watched it with wide eyes.

"It….broke….?" Cornello took it much worse than he did.

"How could this happen?! How could a "pure substance" like the philosopher stone break apart?!" He whimpered pathetically. "I don't know. I don't know anything! Nobody told me a thing!" He whimpered again. "Please spare me. I was wrong. I'm powerless without the stone…Help me…" Yami wasn't paying attention. He was still in wide eyed shock.

"….It's a fake?" He shakily got up. "After coming this far….I thought I could finally go back to normal….And it's a fake…?" He dropped to the ground a few feet away in utter misery and depression. Cornello smirked.

'_Heh, heh, heh…The kid isn't paying attention to me! I'll get even with him even if it means giving everything to kill this one kid!'_ He began to sneak forward, a piece of metal on his arm sharp and pointed so he could skewer Yami.

"Hey…Old man…" Cornello stopped in surprise and anticipation, fear jolting through his heart as he thought that maybe the boy had seen him.

"Uh…Y-yes?" He said, trying to sound innocent. Yami put his hands on the ground, a gentle fizzing of alchemy spreading through the floor.

"First you lied to the townspeople…Then you tried to kill us…" The building started to shake and change shape. "And now, after all the trouble you've put me through…You're telling me the stone was a fake." Cornello looked up with a mixture of fear and awe. "THIS BETTER BE SOME KIND OF JOKE!!" Above Yami's head, was a huge statue of the god Ra, built from a large section of the building, standing up straight and tall, glowering down at Cornello. Yami had one hand on it, using Alchemy to control its movements. "FEEL THE IRON BLOW OF GOD'S WRATH!!" The statue-no-colossus, sent its fist plunging down and struck the ground, its arm cracking a bit from the blow. Aqua came forward.

"It's a fake?" He asked.

"Yeah, it was all a waste of time." Yami sighed, rolling his shadow mail arm while feeling it with his other hand, making sure nothing was wrong with it. "Just when I thought we were going to get our old bodies back." Yami sighed again. Aqua watched Yami's inspection carefully.

"We need to worry about _you_ first. Auto-mail, especially experimental auto-mail, has a lot of problems." Yami stretched, now satisfied that nothing was broken, and finally slumped in defeat.

"Oh well, I guess we'll look somewhere else. Back on the road again" He straightened and prepared to leave.

"But…" Yami looked behind him. Rose was on the ground, her face torn between shock, horror, disbelief, anger, and despair. "I don't understand…There must be a mistake….They told me he could come back to life…" Yami cast a sympathetic look her way.

"Give it up Rose, it could never have been." Rose shook her head in denial.

"What have you done to me…" He whispered, and looked at them. Her face had now decided to go with anger and despair. "What do I do? WHAT AM I SUPPOSED TO BELIEVE IN NOW?!" Tears streamed down her face as she spoke. "Are you going to tell me?!" She couldn't look up anymore and bowed to the ground. "WELL?! ARE YOU?!" Yami let out a small sigh and looked away.

"You…need to figure that out on your own." He looked to Aqua and nodded. They both started walking towards her. "Stand up and walk, keep going forward." He walked by her right side so that she could see his leg of Shadow mail, still exposed by the tear in his leather pants made by the chimera. "At least you have strong legs to take you there." And with that they both left, leaving her to contemplate their words. Rose looked to the sky filled with stars and the setting sun. Tears still streamed down her cheeks, pain and despair deep in her eyes.

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...

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At the bottom of the church, the entire town had gathered in front of the doors. Now an angry mob, they demanded for the one thing that would sate their bloodlust.

"Bring out father Cornello!" One shouted.

"We want the truth!"

"You lied to us!"

"Open up!"

"We want the truth!" The few faithful left put a bar on the doors so that no one could get in. The crowd roared in anger, like some gigantic dragon. Cornello himself was down in the room where he had confronted Yami and Aqua.

"Damn it!" He said, clutching his arm, as it still caused him pain. "I can't believe that runt ruined my plans!" He stomped by the dead chimera, which for some strange reason, looked like something had devoured most of it. The ribs were exposed and a leg was missing. "I won't allow it! I've invested too much in this to let it fall apart."

"Really, you were so close…" Cornello looked up in shock at the new voice. IT was very feminine and seductive. "And now everything's ruined." A beautiful woman was sitting on a man that was grotesquely 

overweight. He was sitting cross-legged on the ground, tearing the skin and meat off of the missing leg of the chimera's. "Long time no see, wish it was longer." The woman had pale skin, long, flowing, golden hair and voluptuous breasts. Her dress was long, but very tight, and colored black, showing a lot of cleavage and revealing a strange tattoo. It was in the shape of a snake swallowing its tail, with tiny wings and a pentagram in the middle. Gloves that went all the way up her arm had red markings of two dots at either end, with double lines running between the two. "You've caused a lot of trouble your holiness." Dark purple eyes gazed at him lazily, half closed in boredom. Cornello finally found his voice.

"Wh-what's the meaning of this?! The philosophers stone you gave me broke into pieces! How dare you give me a fake!" The woman scoffed.

"Oh please, did you honestly think we would hand over the real thing to a person like you?" She got up from the obese man's shoulder. Cornello growled in rage.

"You…you said I could take over this country if I used the stone!" The woman tilted her head in contemplation.

"Hmmm….Yes, I did say something like that didn't I?" The obese man tugged another piece of skin off of the leg. "All we wanted was for you to cause a little bit of chaos in this region, that's all." She laughed openly at the look on Cornello's face. "What? You look surprised! Did you actually believe that a third rate despot like yourself could become the ruler of a country?" She laughed again, mocking him in his naivety. "Ah, ha, ha, ha! You really are too much!" Cornello growled. The obese man dropped the leg of the chimera, pointed to Cornello, and finally spoke in a high, childlike voice.

"Hey Lust! Can I eat this old guy? Can I? Can I?!" Lust chuckled and patted the man on the head.

"No, no Gluttony. You're going to get a stomach ache if you eat the likes of him. If you eat this third rate, no, this fourth rate fool!" That was it, Cornello finally snapped.

"Argh! YOU'RE ALL MOCKING ME! YOU AND EVERYONE ELSE!" He made to punch Lust in the face. Lust pinched the bridge of her nose before swiping her hand. Cornello stopped with a look of shock on his face. Lust's fingers had lengthened and become sharp, and one had passed through his head. She smirked.

"You…are of no more use to us." She pulled her hand back quickly and swung it, the blood on her finger flicking off. Cornello collapsed to the ground, dead. Lust closed her eyes. "Aww…and just when things were going so well." She pulled her fingers back to normal length a sharpness. "Father will be furious. Gluttony picked up the body by the back of its jacket and gazed at the wound. He grinned evilly, and licked his lips, the same tattoo that Lust had on her breast on the center of his tongue. Lust turned back slightly, scratching her temple. "So what should we do next?" She asked.

"Rip! Smack!"

"Hey, I thought I told you not to eat that."

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...

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A whistle blew as a train pulled out of a station, all the cars empty of any passengers. Aqua looked at the vacant seats mildly.

"It seems we're the only ones on board." He said conversationally. Yami looked around with him.

"I heard the rumors, but I didn't know it was _this_ bad." He unfolded the map in his hands, looking out the window. "Guess this isn't exactly tourist country." He looked down at the map. "The town on the eastern border. The Youswell coal mines." The train headed for the mountains, the sun fully set, and the night on its way.

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End Chapter.

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